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Probe/primer details

PNA Tested for in situ hybridization.
Accession no. pB-925
Taxonomy Macrorhabdus ornithogaster; Macrorhabdus; Saccharomycetales incertae sedis; Saccharomycetales; Saccharomycetes; Saccharomycotina; saccharomyceta; Ascomycota; Dikarya; Fungi; Opisthokonta; Eukaryota
Specificity Macrorhabdus ornithogaster
Category eukaryotes
Target rRNA 18S rRNA
Position 704-718
Sequence 5'- AAT TGA ACC AGG ACG -3'
G+C content [%] 47
Length [nt] 15
Check specificity/coverage
Formamide [%] 20
Hybridization efficiency

Phylogenetic analysis identifies the 'megabacterium' of birds as a novel anamorphic ascomycetous yeast, Macrorhabdus ornithogaster gen. nov., sp. nov. Tomaszewski EK, Logan KS, Snowden KF, Kurtzman CP, Phalen DN. International journal of systematic and evolutionary microbiology. 2003. Pubmed

Remarks In situ hybridization with a commercially synthesized peptide nucleic acid (PNA) probe.


Name (Alm et al., 1996). Probe designation according to Alm, E. W., Oerther, D. B., Larsen, N., Stahl, D. A., Raskin, L. (1996). The oligonucleotide probe database. Appl Environ Microbiol 62: 3557-9. Abstract (PUBMED).
Position. Probe position according to the E. coli gene numbering.
Sequence. Sequence in IUPAC code: R=G/A, Y=T/C, M=A/C, K=G/T, S=G/C, W=A/T, H=A/C/T, B=G/T/C, V=G/C/A, D=G/A/T, N=G/A/T/C
Tm. Dissoziation temperature according to: Tm=64.9 + 41 x ((G + C - 16.4)/length).
Hybridization efficiency. Use this tool to assess in silico sensitivity (i.e. the hybridization efficiency of the oligonucleotide with its fully complementary target sequence, calculated with ProbeMelt.
Formamide. Percent formamide in the hybridization buffer for optimal hybridization conditions in FISH experiments.
Coverage. Coverage of the three domains calculated using the SILVA reference database 106 if no or a single mismatch is allowed. The detailed method is described in Klindworth et al., 2012. Nucleic Acids Res. 10.1093/nar/gks808 Full Text
Check specificity/coverage. Use these options to reveal the in silico specificity (i.e. number of matching rRNA sequences outside the target taxon) and coverage (i.e. percentage of matching rRNA sequences within the target taxon) of an oligonucleotide against the most recent SSU and LSU rRNA sequence databases.